Package: genefu

Version: 2.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:genefu.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings genefu_2.15.0.tar.gz

StartedAt: 2019-04-09 02:09:39 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:12:57 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 198.2 seconds

RetCode: 0

Status:  OK

CheckDir: genefu.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:genefu.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings genefu_2.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/genefu.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genefu’ version ‘2.15.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'survcomp', 'mclust', 'limma', 'biomaRt', 'iC10', 'AIMS'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genefu’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘mclust:::grid1’ ‘mclust:::grid2’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
claudinLow: no visible global function definition for ‘standardize’
Undefined global functions or variables:
  standardize
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘multilevel’, ‘dplR’
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/genefu.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL genefu
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘genefu’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genefu)

name	user	system	elapsed
bimod	0.172	0.032	0.205
boxplotplus2	0.036	0.001	0.038
claudinLow	1.075	0.032	1.108
claudinLowData	0.025	0.006	0.031
compare.proto.cor	1.203	0.042	1.246
compute.pairw.cor.meta	1.783	0.086	1.869
compute.proto.cor.meta	1.054	0.067	1.122
cordiff.dep	0.016	0.004	0.020
endoPredict	0.024	0.006	0.030
expos	0.004	0.005	0.009
fuzzy.ttest	0.002	0.001	0.003
gene70	0.181	0.024	0.205
gene76	0.036	0.006	0.043
geneid.map	0.060	0.008	0.068
genius	0.268	0.062	0.329
ggi	0.066	0.011	0.077
ihc4	0.010	0.008	0.017
intrinsic.cluster	0.294	0.024	0.299
intrinsic.cluster.predict	0.186	0.022	0.208
map.datasets	0.908	0.023	0.931
mod1	0.002	0.002	0.005
mod2	0.002	0.002	0.005
modelOvcAngiogenic	0.002	0.003	0.005
molecular.subtyping	3.890	0.306	4.220
nkis	0.003	0.004	0.007
npi	0.011	0.009	0.020
oncotypedx	0.087	0.021	0.107
ovcAngiogenic	0.122	0.027	0.149
ovcCrijns	0.082	0.007	0.088
ovcTCGA	0.285	0.014	0.298
ovcYoshihara	0.084	0.013	0.098
pam50	0.037	0.009	0.046
pik3cags	0.078	0.008	0.087
power.cor	0.001	0.000	0.001
ps.cluster	0.502	0.031	0.502
read.m.file	0.040	0.003	0.046
rename.duplicate	0.003	0.001	0.004
rescale	0.089	0.021	0.110
rorS	0.174	0.016	0.190
scmgene.robust	0.007	0.003	0.010
scmod1.robust	0.010	0.004	0.014
scmod2.robust	0.010	0.005	0.014
setcolclass.df	0.003	0.000	0.003
sig.endoPredict	0.008	0.005	0.013
sig.gene70	0.006	0.005	0.011
sig.gene76	0.007	0.003	0.010
sig.genius	0.033	0.012	0.045
sig.ggi	0.006	0.002	0.009
sig.oncotypedx	0.004	0.002	0.007
sig.pik3cags	0.004	0.002	0.006
sig.score	0.074	0.012	0.086
sig.tamr13	0.010	0.009	0.019
sigOvcAngiogenic	0.008	0.004	0.011
sigOvcCrijns	0.009	0.005	0.013
sigOvcSpentzos	0.007	0.003	0.009
sigOvcTCGA	0.032	0.009	0.040
sigOvcYoshihara	0.011	0.006	0.015
spearmanCI	0.000	0.000	0.001
ssp2003	0.036	0.007	0.044
ssp2006	0.06	0.01	0.07
st.gallen	0.013	0.008	0.023
stab.fs	0.187	0.008	0.196
stab.fs.ranking	1.335	0.165	1.500
strescR	0.001	0.001	0.002
subtype.cluster	0.458	0.068	0.529
subtype.cluster.predict	0.194	0.043	0.238
tamr13	0.081	0.010	0.091
tbrm	0	0	0
vdxs	0.004	0.004	0.008
weighted.meanvar	0.001	0.001	0.000
write.m.file	0.003	0.003	0.006